RetrogeneDB ID: retro_xmac_3

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556902.1:662375..663701(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019883
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: pspc1
• Ensembl ID: ENSXMAG00000007929
• Aliases: None
• Description: paraspeckle component 1 [Source:ZFIN;Acc:ZDB-GENE-030131-9530]

Sequence

>retro_xmac_3
CAAAACATGCAAGGCTACAGAGGCCCCCAACAGAACCACGGCCCCAACCGTCCGGGGAACCACCTCAAAGGCGACGGGCC
CAACAGCAACGGACAGCAGCCGGAGCCTAGCGAGCAGACCAGCCCCAACGCGGGCTTGACGCTGGACCCGCAGAGCTTCA
GGAAGCCCGGAGAGAAAACCTTCACCCAGCGGAGCAGGCTGTTCGTGGGGAACCTGCCCACCGGAGTCACCGAGGAGGAG
CTGGTCAAGCTGTTCGCGAAGTACGGGAACGCCAGCGAGATCTTCGTCAACAAGGACAGGGGGTTCGGGTTCATCCGCCT
GGAGACCAGGATCATCGCGGAGATCGCCAGAGCGGAGTTGGATGATTTCGTGTTCAAAGGCAGACCCATCCGGGTGAGGT
TCGCCACACACGGCGCCGCTTTGTCCGTGAAAAACCTCCCGGAGTTTGTGTCCAACGAGCTCCTGGAGGAGGCCTTCTCC
GTCTTCGGCCAGATAGAGAGGGCTCTGGTGATCGTGGATGACCGGGGCAGGCCCACGGGGAAAGGCATCGTGGAGTTCAC
CGCGAAGCCAGCCGCTAGGAAAGCTCTAGATAAGTGCAACGACAGCGCCTACCTCCTCACAGCGTTCCCCCGGCCCGTCA
CCGTGGAGCCCATGGAGCAGTACGACGAGGACGAGGGTCTGCCGGAGAAGCTGATCAACAGGAACCAGCAGTACCACAAG
GAGCGCGAACAGCCCCCGCGGTTCGCCCAGCCCGGCTCGTTCGAGTACGAGTACGCCATGCGCTGGAAAGCCCTGATGGA
GATGGAGAAGCAGCAGTACGAGATGGTCGACCGCAACATGAAGGAGGCGCAGGAGAAGCTGGAGGCCGAGATGGAGGCGG
CCAGACACGAGCACCAGGTGATGCTGATGAGGCAGGACCTGCTGAGGAGACAGGAGGAGCTGCGGAGGATGGAGGAACTC
CACAACCAGGAGGTGCAGAAGAGGAAGCAGGCCGAGCTGAGGCAGGAGGAGGAGCGCCGGAGGAGAGAAGAGGAGATGAG
GCTGCGCAACGAGGAGATGATGAAGAGGCAGCAGGAGGGCTTCAGGGGCGGCTTCCCTGAGAACAGAGAGCAGGAGATGA
GGATGCACATGGGGGGCCACGGCATGGCCATGAACAGAAATTCCCTGGGTGGGAACTCGGGTGCCGCCGGCGCTGCTGGC
ATGGCCGCCGAGAGCGCTCCTATGATGGCGGGCTCAGGTAGCGGCAGCCTGCCCGGAGGGGGCCAGGGCGGCTTCCCCAG
AGGGCTCCCCGGCCCCGGAGACTATAGCAAGCAGCGCAGATTTTGA

Alignment

ORF - retro_xmac_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.44 %
• Parental protein coverage: 77.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKGSPAPPQQQSPAADQSEGAAEETGECPSK---MTLDIASFRKPGEKTFTQRSRLFVGSLPLDITEEEF
          N.G...P..........S.G...E..E..S.....TLD..SFRKPGEKTFTQRSRLFVG.LP...TEEE.
Retrocopy NHGPNRPGNHLKGDGPNSNGQQPEPSEQTSPNAGLTLDPQSFRKPGEKTFTQRSRLFVGNLPTGVTEEEL

Parental  RNLFAKYGNINEVFINRERGFGFVCLETRTLAEIAKVELDGSVLSNRALKVRFATHGAALKVRNLLPVVT
          ..LFAKYGN..E.F.N..RGFGF..LETR..AEIA..ELD..V...R...VRFATHGAAL.V.NL...V.
Retrocopy VKLFAKYGNASEIFVNKDRGFGFIRLETRIIAEIARAELDDFVFKGRPIRVRFATHGAALSVKNLPEFVS

Parental  NELLEEAFSQFGPVERAIVVTDDRGRSTGRGIVEFASKVAARKALERCNEGAMLLTTTPCPTIVEPMEHL
          NELLEEAFS.FG..ERA.V..DDRGR.TG.GIVEF..K.AARKAL..CN..A.LLT..P.P..VEPME..
Retrocopy NELLEEAFSVFGQIERALVIVDDRGRPTGKGIVEFTAKPAARKALDKCNDSAYLLTAFPRPVTVEPMEQY

Parental  DDEDGLPEKILPKTPKYYKEREQTPRFAQPGTFEFEYASRWKALDEMEKQQREQVDRNIKEAREKLEAEL
          D...GLPEK.......Y.KEREQ.PRFAQPG.FE.EYA.RWKAL.EMEKQQ.E.VDRN.KEA.EKLEAE.
Retrocopy DEDEGLPEKLINRNQQYHKEREQPPRFAQPGSFEYEYAMRWKALMEMEKQQYEMVDRNMKEAQEKLEAEM

Parental  EAAKNEHQLMLMRQDLLRRQEELRRLEELRNQELQRRKQIEMRHEEERRRREEEMMRHREQDELRRQPDG
          EAA..EHQ.MLMRQDLLRRQEELRR.EEL.NQE.Q.RKQ.E.R.EEERRRREEE.MR.R......RQ...
Retrocopy EAARHEHQVMLMRQDLLRRQEELRRMEELHNQEVQKRKQAELRQEEERRRREEE-MRLRNEEMMKRQQE-

Parental  GGFVPNYHENREQEMRVGELGPRGAGNMGD-GFNQASGGPSG---NQGQMMGGSGRG
          .GF.....ENREQEMR....G...A.N....G.N....G..G.......MM.GSG.G
Retrocopy -GFRGGFPENREQEMRMHMGGHGMAMNRNSLGGNSGAAGAAGMAAESAPMMAGSGSG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_3 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_3 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011078	2 retrocopies	retro_dnov_1278, retro_dnov_488,
Tupaia belangeri	ENSTBEG00000002361	2 retrocopies	retro_tbel_2388, retro_tbel_3616,
Xiphophorus maculatus	ENSXMAG00000007929	1 retrocopy	retro_xmac_3 ,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,